Complete Genome Sequence of Candida theae from Hickman Line Infection in an Immunocompromised Child
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MYCOPATHOLOGIAGENOME
Complete Genome Sequence of Candida theae from Hickman Line Infection in an Immunocompromised Child
Received: 20 January 2020 / Accepted: 6 July 2020 / Published online: 23 July 2020 Ó Springer Nature B.V. 2020
Abstract We present the first whole-genome-sequencing data of a rare fungal species, Candida theae isolated in the context of a Hickman line infection in a patient with juvenile myelomonocytic leukaemia. To our knowledge, this is the first instance of publicly available genomic data for this species. Loci associated with antifungal resistance were referenced against its closely related members of the Candida parapsilosis complex. Keywords Whole-genome-sequencing Candida theae Antifungal susceptibility 5-Flucytosine resistance Antimicrobial resistance
Candida theae was first described in 2012 from Indonesia and Ecuador [1] and is genetically most closely related to the Candida parapsilosis complex, with only 1.1–1.7% nucleotide difference in the D1/ D2 domain of the large subunit (LSU) rDNA. Other than two cases of C. theae candidaemia reported in a study from Shanghai, China [2], there were no other identified clinical reports of C. theae infections. A 5-year-old boy with Juvenile Myelomonocytic Leukaemia was admitted for non-neutropaenic fever following flushing of his Hickman line. The patient had a previous splenectomy and underwent peripheral blood stem cell transplant 6 months prior to this episode. No distant foci of infections were identified.
Tip cultures of the Hickman line grew C. theae on blood and chocolate plates under aerobic conditions. Subculture on Sabouraud dextrose medium and CHROMagar Candida did not demonstrate any distinct morphological features (Supplementary Figure 1). Bruker MALDI-TOF Biotyper (Bruker Daltonik GmbH, Breman, Germany) and Vitek MS (bioMe´rieux, Marcy-l’E´toile, France) both could not identify the Candida isolate. Sequencing of the internal transcribed spacer (ITS) performed as previously described [3] identified the isolate as C. theae with a 99.6% nucleotide identity to the ITS region of C. theae type strain ATCC MYA-4746 (GenBank Accession No. NR_111722.1). For further confirmation, whole-genome sequencing of the isolate was carried out. Illumina HiSeq was used to generate 150 bp paired-end reads and assembled using Shovill v1.0.4 (https://github.com/tseemann/shovill). Longread sequencing was performed using a MinION sequencer (Oxford Nanopore Technologies) then assembled using Canu v1.8 [4], polished with Pilon v1.23 [5]. The resulting assembly was further polished using quickmerge [6] to improve its contiguity. Finally, QUAST v5.0.2 was used to evaluate the quality of the genome assembly [7]. Assembly statistics were: 80 contigs, assembly length of 13,095,904 bp, and N50 of 521,980 bp. This Whole Genome Shotgun project has been deposited at DDBJ/ ENA/GenBank under the accession JABBGN000000000. The version described in this
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paper is version JABBGN010000000. The isolate has be
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